What is this about?
Beacon API specification:
What else is out there?
Beacon Development Kits (BDK)
• Open-source quickstarts.
• Compliant with the latest beacon specification.
• Proven to work well.
• Available in:
• Most advanced of the BDKs.
• Effectively a reference implementation.
• Compatible beacon API.
• Sample beacon implementation.
• Integration of Beacon data models.
• Various utilities: output serialization, input normalization, error
handling and status code mapping…
• Test suite.
• Security (prototype).
BDK adapter system
• Adapter API:
• Adapter implementations for common data stores/APIs:
• 3 adapters OOTB:
• Variants API
• variant set beacon dataset
• Annotation API
• annotation set beacon dataset
• file beacon dataset
• Easy to implement your own and plug into Java BDK.
• Extension of Java BDK for more complex beaconizing.
• Support for multiple adapters and multiple beacons.
• Open-source: https://github.com/mcupak/beaconizer
• Query beacons from Java.
• Integration with Beacon 0.3 schema.
• Open-source: https://github.com/mcupak/beacon-client
• Query beacons from your shell.
• Open-source: https://github.com/mcupak/beacon-cli
$ java -jar beacon-cli.jar -u http://localhost:5000/test/ response —help
Description: Gets response to a beacon query for allele information.
-a (--assembly-id) VAL : Assembly ID (GRC notation, e.g. 'GRCh37').
-ab (--alternate-bases) VAL : The bases that appear instead of the
reference bases. Accepted values: see the
ALT field in VCF 4.2 specification
$ java -jar beacon-cli.jar -u http://localhost:5000/test/ response
-a GRCh37 -ab A -r 1 -rb T -s 1000
• Test beacon compatibility with 0.3 specification.
• Groovy-based prototype.
• Open source: https://github.com/mcupak/beacon-compliance
• Coordinate conversion library.
• Wraps Liftover and HGVS.
• Extensible, with built-in converters for standard assemblies.
• Open-source: https://github.com/mcupak/genome-coordinates-
Any tools we’re missing?
Huge thanks to the Beacon team and our summer students Patrick and Artem.